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Biochem 1Bi2LE > Ch35 - DNA Organization, Replication, And Repair > Flashcards

Ch35 - DNA Organization, Replication, And Repair Flashcards

1
Q

Most abundant chromatin proteins

A

Histones

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3
Q

Consists of very long double stranded (dsDNA) molecules, histones, nonhistone proteins, and RNA

A

Chromatin

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4
Q

Characteristic of the 2/3 of histone molecules

A

Hydrophobic

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5
Q

Composed of DNA wound around an octameric complex of histone molecules

A

Nucleosome

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6
Q

4 major types of histones

A

H2A, H2B, H3, and H4

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8
Q

They form a tertamer containing 2 molecules of each

A

H3 and H4

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10
Q

145 bp of DNA and 1.75 superhelical turns

A

Octamer

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11
Q

Rhe core histones are subject to 6 types of covalentmodification or posttranslational modifications

A

Acetylation, methylation, phosphorylaton, ADP-ribosylaton, monoubiquitylation, and sumoylation

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12
Q

Acetylation of histones H3 and H4

A

Activation or inactivation of gene transcription

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14
Q

Acetylation of core histones

A

Chromosomal assembly during DNA replication

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15
Q

Involved in DNA replication and repair, and the proteins involved in RNA synthesis, processing, and transport to the cytoplasm

A

Nonhistone proteins

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16
Q

Phosphorylation of histone H1

A

Condensation of chromosomes

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17
Q

Sumoylation

A

Transcription repression

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18
Q

Amino terminal thirds of histones

A

Amino acids

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19
Q

Can confer nucleosome-like properties on DNA and thus has a central in the formation of the nucleosome

A

H3-H4 tetramer

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20
Q

ADP-ribosylation of histones

A

DNA repair

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21
Q

Condenses DNA

A

Histones

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22
Q

Stabilizes the primary particle and binds firmly two additional half-turns of DNA

A

H2A - H2B dimers

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23
Q

Group of proteins that exhibit high affinity fot binding histones

A

Histone chaperones

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24
Q

Methylation of histones

A

Activation and repression of gene transcription

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25
Q

Physical flexibility of particular nucleotide sequences to accommodate the regions of kinking within the supercoil

A

Phasing

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26
Q

2 higher order structures that provide compaction of chromatins

A

10nm fivtil and 30nm chromatin fiber

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27
Q

Consists of nucleosome arranged with their edges separated by a small distance with their flat faces parallel to the fibril axis

A

10nm fibril

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28
Q

This is formed when 10nm fibril is supercoiled with six or seven nucleosomes per turn

A

30nm fibril

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29
Q

Stabilizes the 30nm fiber

A

H1 histones

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30
Q

DNA in active chromatin contains large regions that are more sensitive to digestion by a nuclease such as…

A

DNase I

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31
Q

Shirter stretsches if 100-300 nucleotides that exhibit an even greater sensitivity to DNase I

A

Hypersensitive sites

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32
Q

Often located immediately upstream from the active gene and are the location of uninterrupted nucleosome structure caused by binding of nonhistone proteins

A

Hypersensitive sites

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33
Q

Densely packed during interphase

A

Inactive chromatin

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34
Q

Inactive chromatin

A

Heterochromatin

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35
Q

Active chromatin

A

Euchromatin

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36
Q

Type of heterochromatin that is always condensed and thus inactive

A

Constitutive heterochromatin

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37
Q

Type of heterochromatin that is at times dense, and other times actively transcribed

A

Facultative heterochromatin

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38
Q

In insects, chromosomes that have been replicated for multiple cycles wothout separation of daughter chromatids

A

Polytene chromosomes

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39
Q

Adenine-thymine-rich region containing repeated DNA sequences that range in size

A

Centromere

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40
Q

Nucleosomes containing the histone H3 variant protein CENP-A

A

Kinetochore

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41
Q

Provides the anchor for mitotic spindle

A

Kinetochore

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42
Q

Ends of each chromosome

A

Telomeres

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43
Q

Consist of short TG-rich repeats

A

Telomeres

44
Q

Enzyme responsible for telomere synthesis and thus in maintaining the length of the telomere

A

Telomerase

45
Q

Proteins that constitute integral components of the inner nuclear membrane within the nucleus

A

Lamins

46
Q

Noncoding regions

A

Introns

47
Q

Coding regions

A

Exons

48
Q

DNA in eukaryoric genome can be dicided into 2 broad sequence classes

A

Unique sequence (nonrepetitive) and repetitive-sequence DNA

49
Q

Repititive seauences that are often clustered in centromeres and telomeres

A

Highly repetitive sequences

50
Q

Repetitive sequences that are not clustered but are intessperesed with unique sequences

A

Moderately repetitive sequences

51
Q

Arise from movement of one location to another (transposition) through an RNA intermediate by the action od reverse transcriptase that transcribes an RNA template into DNA

A

Retrospons

52
Q

Integral components of mRNA precursors or as discrete RNA molecules

A

Alu family (SINEs)

53
Q

Transposition events as the insertion of ALU sequences into a gene, when mutated can cause…

A

Neurofibromatosis

54
Q

SINE RNA that rehulate mRNA productions at the levels of transcription and mRNA splicing

A

Alu B1 and B2

55
Q

Found as dinucleotide repeats of AC on one strand and TG on the opposite strand

A

Microsatellite sequences

56
Q

Used in detecting microsatellite sequences

A

Polymerase chain reaction (PCR)

57
Q

Trinucleotide sequence CGG repeat sequence is associated with this disease

A

Fragile X syndrome

58
Q

Insertions or deletions od purine and pyrimidine bases

A

Indels

59
Q

Exchange between similar or homologous chromosomes of genetic information

A

Recombination

60
Q

Occur primarily during meiosis in mammalian cells and requires realignment of homologous metaphase chromosomes

A

Recombination

61
Q

Affects tandem arrays of repeated DNAs whether they are related globin genes or more abundant repetitive DNA

A

Unequal crossover

62
Q

Jumping genes, can carry flanking regions of DNA

A

Jumping DNA

63
Q

Consist of DNA sequences identical or nearly identical to those of the messenger RNA for the appropriate gene product

A

Processed genes

64
Q

Processed genes confaining nonsense codons

A

Pseudogenes

65
Q

Accidental fixation of one variant or another throughout a family of reoeated sequences and thereby homogenize the sequences of the members of repetitive DNA families

A

Gene conversion

66
Q

There is an association of sequence-specific dsDNA-binding proteins with a series of direct repeat DNA sequences

A

Origin of replication

67
Q

In E.coli, the oriC is bound by the protein…

A

dnaA

68
Q

Origin of replication in yeast and is bound by the MCM protein complex

A

DNA unwinding element

69
Q

Replication for consists of 4 components

A

DNA helicase, SSBs bind to ssDNA, primase, DNA polymerase

70
Q

Binds to template DNA as a part of multiprotein complex that consists of several polymerase accessory factors

A

Dna poymerase III enzyme

71
Q

Mobioe complex between helicase and primase

A

Primosome

72
Q

Rate at which polymerization occurs

A

Chain elongation

73
Q

Expression of the number of nucleotides added to the nascent chain before the polymerase disengages from the template

A

Processivity

74
Q

Mostly involved in proofreading and DNA repair

A

Pol I and pol II

75
Q

Inititation of DNA synthesis requires priming by a short lenght of RNA. In E.coli, this is catalyzed by…

A

dnaG primase

76
Q

In eukaryotes, the initiation of DNA synthesis is catalyzed by…

A

DNA Pol a

77
Q

This process involves nucleophilic attack by the 3’-hydroxyl group of the RNA primer on the phosphate of the first entering deoxynucleoside triphosphate

A

Priming

78
Q

Seals the fragments of newly synthesized DNA

A

DNA ligase

79
Q

Replication of the lagging strand

A

Semidiscontinous DNA synthesis

80
Q

The entire mammalian genome replicates in approximately how many hours

A

9 hrs

81
Q

In bacteria, Replication occurs in both direction along all of the chromosomes, and both strands are replicated simultaneously. This replication process generates…

A

Replication bubbles

82
Q

In E.coli, separation of DNA strands is promoted by…

A

SSBs

83
Q

In eukaryotes, separation of DNA strands is promoted by…

A

Replication protein A (RPA)

84
Q

Protein complex that unwinds DNA in E.coli

A

DNAB protein complex

85
Q

Unwinds eukaryotic DNA

A

Hexameric MCM complex

86
Q

Nicking resealing enzymes

A

DNA topoisomerases

87
Q

Capable of unwinding supercoiled DNA

A

Topoisomerases

88
Q

Enzymes capable of synthesizing a single strand and then a dsDNA molecule from a single-stranded DNA template

A

RNA-dependent DNA polymerase or reverse transcriptase

89
Q

Core particles are separated by roughlt 30-bo region of DNA

A

Linker

90
Q

Monoubiquitylation

A

Gene activation, repression, and heterochromatic gene silencing

91
Q

Form dimers

A

H2A and H2B

95
Q

Histone that is least tightly bound to chromatin. Easily removed with salt solution

A

H1 histones

96
Q

This is a specific virus encoded nuclease, that degrades the hybridized template RNA strand

A

RNase H

97
Q

DNA synthesis occurs during what phase of the cell cycle

A

S phase

98
Q

Family of proteins whose concentration increases and decreases at specific times

A

Cyclins

99
Q

Phosphorylate substrates essential for progression through the cell cycle

A

Cyclin-dependent protein kinases (CDKs)

100
Q

Once chromatin has been replicated, it is marked so as to prevent its further replication until it again passes through mitosis

A

Replication licensing

101
Q

Five major DNA repair pathways in eukaryotic cells

A 
Nucleotide excision repair (NER)
Mismatch repair (MMR)
Base excision repair (BER)
Homologous recombination (HR)
Nonhomologous end-joining (NHEJ)
102
Q

What repair pathway?

Double strand breaks

A

HR and NHEJ

103
Q

Plays a key role in both G1 and G2 checkpoint control

A

Tumor supressor p53

104
Q

Cdk-cyclin inhibitor

A

P21

Biochem 1Bi2LE (4 decks)

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